ArticleNucleic acids research2022
3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 2 of them syntheses that pooled it.
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41 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- The Variant rs2706682 at PITPNC1, Which Enhances Vehicular Secretion, Associated With Systemic Lupus Erythematosus Susceptibility in Chinese Populations.International journal of immunogenetics · 2026Article
- Molecular regulatory mechanisms of schizophrenia-associated functional non-coding variants.Molecular psychiatry · 2026Article
- [Association analysis between dystrophin gene polymorphism and non-syndromic cleft lip with or without cleft palate].Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology · 2026Article
- Potentially Functional Variants in FCER1A and PLCG2, Two B Cell-Related Immune Genes Predict the Survival of Chinese Gastric Cancer Patients.Molecular carcinogenesis · 2026Article
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- Genetic variations interact with polybrominated diphenyl ether exposure to alter lipid homeostasis.Nature communications · 2026Article
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- Trans-ancestry genome-wide analyses of bipolar disorder in East Asian and European populations improve genetic discovery.Nature neuroscience · 2026Article
- Identification of rs28362336 as a risk SNP for generalized myasthenia gravis and its impact on HCG27 regulation.PloS one · 2026Article
- [Correlation betweenZhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences · 2025Article
- Genome-wide insights of shared genetic architecture between menstrual traits and bone mineral density.Endocrine connections · 2025Article
- Association Between Primary Dysmenorrhea and Mental Health Traits: A Study Based on Multi-Phenotype Correlation Network and Mendelian Randomization Analysis in Female College Students.Phenomics (Cham, Switzerland) · 2025Article
- Genetic determinants of monocyte splicing are enriched for disease susceptibility loci.Nature communications · 2025Article
- Association of ZNF608 Polymorphisms With House Dust Mite-Induced Allergic Rhinitis.Clinical and translational allergy · 2025Article
- Gene-Smoking Interaction in Insulin Sensitivity and β-Cell Function Among Normal Glucose Tolerance Individuals.Journal of diabetes · 2025Article
- Identification of Schizophrenia-Risk Regulatory Variant rs1399178 in the Non-coding Region With Its Impact on NRF1 Binding.CNS neuroscience & therapeutics · 2025Article
- Genetic predisposition to Behcet's disease mediated by a IL10RA enhancer polymorphism.Heliyon · 2025Article
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5 authors.
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Abstract
The rapid development of single-molecule long-read sequencing (LRS) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) technologies presents both challenges and opportunities for the annotation of noncoding variants. Here, we updated 3DSNP, a comprehensive database for human noncoding variant annotation, to expand its applications to structural variation (SV) and to implement variant annotation down to single-cell resolution. The updates of 3DSNP include (i) annotation of 108 317 SVs from a full spectrum of functions, especially their potential effects on three-dimensional chromatin structures, (ii) evaluation of the accessible chromatin peaks flanking the variants across 126 cell types/subtypes in 15 human fetal tissues and 54 cell types/subtypes in 25 human adult tissues by integrating scATAC-seq data and (iii) expansion of Hi-C data to 49 human cell types. In summary, this version is a significant and comprehensive improvement over the previous version. The 3DSNP v2.0 database is freely available at https://omic.tech/3dsnpv2/.
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